SAXSdb — 5xxp

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1. Protein Identity and Related Structures Protein Identity & Related Structures

LysR-type regulatory protein

Cupriavidus necator

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 2	DNA (25-MER) × 1 DNA (25-MER) × 1 water × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9WXC7_CUPNE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–87； UniProt 1–87 Author chain B； PDBConstruct 1–87； UniProt 1–87

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5xxp
Deposition date deposition_date	2017-07-04
Structure title title	Crystal structure of CbnR_DBD-DNA complex
Keywords keywords	DNA complex, DNA binding domain, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5xxp__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5xxp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5xxp__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	23.84 Å
Rg (electron density)	22.69 Å
Total Rg	23.35 Å
Atom count	2333
Residues	224
Excluded volume	38184 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5xxp__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	LysR-type regulatory protein
Molecular weight formula_weight	11321.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2335

MEFRQLKYFIAVAEAGNMAAAAKRLHVSQPPITRQMQALEADLGVVLLERSHRGIELTAAGHAFLEDARRILELAGRSGDRSRAAARENLYFQGAHHHHHH

Source Source

Source organism organism	Cupriavidus necator
Common name common_name	Alcaligenes eutrophus
NCBI taxonomy ID ncbi_taxonomy_id	106590
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DNA (25-MER)
Molecular weight formula_weight	7651.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

CTATATTACGCAAACCGTAACGATG

Entity 3 Entity 3 polymer

Description description	DNA (25-MER)
Molecular weight formula_weight	7704.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

CATCGTTACGGTTTGCGTAATATAG

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

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Unit-cell length a length_a	186.457 Å
Unit-cell length b length_b	28.719 Å
Unit-cell length c length_c	73.153 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.65 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	67.990 Å
R factor r_factor	0.2216
R_work r_work	0.2194
R_free r_free	0.2633

Crystal structure of CbnR_DBD-DNA complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

LysR-type regulatory protein

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5xxp__assembly_1__model_1

5xxp__assembly_1__model_1 | I(q)

5xxp__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

7. Citations (1)

Crystal structure of CbnR_DBD-DNA complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

LysR-type regulatory protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5xxp__assembly_1__model_1

5xxp__assembly_1__model_1 | I(q)

5xxp__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

7. Citations (1)